After remove nodes from repository still remain files "file_name.modeshape" with content:

modeint:nodeDefinition (string) "

{httpwww.modeshape.org1.0}

root//

{httpwww.jcp.orgjcrnt1.0}

base"

To reproduce this issue run RepositoryClientTest test. After succesfully test execution in "fileSystemSource/fileSystemWorkspace" directory remain file "test.file.modeshape".